6 Nov
2014
6 Nov
'14
3:23 p.m.
Hi! I have several external regressors in my analysis that I configure with -taskreg in mkanalysis-sess (something like -notask -taskreg nameoffile 6). I was wondering how to set up mkcontrast-sess to contrast these regerssors given that I do not have a paradigm file for them. Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5?
Thanks, Caspar
10 Nov
10 Nov
1:36 p.m.
Hi! A quick follow-up: I have a taskreg file with 6 continuous predictors. I would like to run specific contrasts, e.g., predictor 1 vs. mean(predictor 2:6).
From what I gather, selxavg3-sess will run automatic contrasts on taskregs,
but the automatic contrasts are against baseline. This is not what I need at this point. mk-contrast-sess does not like what I am putting in because I do not have a paradigm file in which condition numbers are specified. Is there a way to compute specific contrasts between multiple taskregs, and if not, is there a workaround? Thank you very much, Caspar
2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik <cschwiedrz@rockefeller.edu
:
Hi! I have several external regressors in my analysis that I configure with -taskreg in mkanalysis-sess (something like -notask -taskreg nameoffile 6). I was wondering how to set up mkcontrast-sess to contrast these regerssors given that I do not have a paradigm file for them. Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5?
Thanks, Caspar
1:45 p.m.
To get sig maps for an individual, this is problematic but I could probably come up with a work-around. For a group analysis, you can simply compute each taskreg separately, then subtract the two prior to running mri_glmfit. doug
On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote:
Hi! A quick follow-up: I have a taskreg file with 6 continuous predictors. I would like to run specific contrasts, e.g., predictor 1 vs. mean(predictor 2:6). From what I gather, selxavg3-sess will run automatic contrasts on taskregs, but the automatic contrasts are against baseline. This is not what I need at this point. mk-contrast-sess does not like what I am putting in because I do not have a paradigm file in which condition numbers are specified. Is there a way to compute specific contrasts between multiple taskregs, and if not, is there a workaround? Thank you very much, Caspar
2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik <cschwiedrz@rockefeller.edu mailto:cschwiedrz@rockefeller.edu>:
Hi! I have several external regressors in my analysis that I configure with -taskreg in mkanalysis-sess (something like -notask -taskreg nameoffile 6). I was wondering how to set up mkcontrast-sess to contrast these regerssors given that I do not have a paradigm file for them. Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5? Thanks, Caspar
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
1:54 p.m.
Hi Doug, thanks for your reply. I would like to feed the differences into a FFX group analysis, so I think I will need to resort to your workaround. It would be great if you could provide that. Thanks! Caspar
2014-11-10 13:45 GMT-05:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
To get sig maps for an individual, this is problematic but I could probably come up with a work-around. For a group analysis, you can simply compute each taskreg separately, then subtract the two prior to running mri_glmfit. doug
On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote:
Hi! A quick follow-up: I have a taskreg file with 6 continuous predictors. I would like to run specific contrasts, e.g., predictor 1 vs. mean(predictor 2:6). From what I gather, selxavg3-sess will run automatic contrasts on taskregs, but the automatic contrasts are against baseline. This is not what I need at this point. mk-contrast-sess does not like what I am putting in because I do not have a paradigm file in which condition numbers are specified. Is there a way to compute specific contrasts between multiple taskregs, and if not, is there a workaround? Thank you very much, Caspar
2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik <cschwiedrz@rockefeller.edu mailto:cschwiedrz@rockefeller.edu>:
Hi! I have several external regressors in my analysis that I configure with -taskreg in mkanalysis-sess (something like -notask -taskreg nameoffile 6). I was wondering how to set up mkcontrast-sess to contrast these regerssors given that I do not have a paradigm file for them. Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5? Thanks, Caspar
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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11 Nov
11 Nov
11:56 a.m.
Hi Doug, I wanted to follow up on this. Would you be able to provide a workaround for contrasting multiple taskregs against each other? Is there something I can try in the meantime? Thanks, Caspar
2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik <cschwiedrz@rockefeller.edu
:
Hi Doug, thanks for your reply. I would like to feed the differences into a FFX group analysis, so I think I will need to resort to your workaround. It would be great if you could provide that. Thanks! Caspar
2014-11-10 13:45 GMT-05:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
To get sig maps for an individual, this is problematic but I could probably come up with a work-around. For a group analysis, you can simply compute each taskreg separately, then subtract the two prior to running mri_glmfit. doug
On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote:
Hi! A quick follow-up: I have a taskreg file with 6 continuous predictors. I would like to run specific contrasts, e.g., predictor 1 vs. mean(predictor 2:6). From what I gather, selxavg3-sess will run automatic contrasts on taskregs, but the automatic contrasts are against baseline. This is not what I need at this point. mk-contrast-sess does not like what I am putting in because I do not have a paradigm file in which condition numbers are specified. Is there a way to compute specific contrasts between multiple taskregs, and if not, is there a workaround? Thank you very much, Caspar
2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik <cschwiedrz@rockefeller.edu mailto:cschwiedrz@rockefeller.edu>:
Hi! I have several external regressors in my analysis that I configure with -taskreg in mkanalysis-sess (something like -notask -taskreg nameoffile 6). I was wondering how to set up mkcontrast-sess to contrast these regerssors given that I do not have a paradigm file for them. Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5? Thanks, Caspar
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
12:04 p.m.
Actually, you can still do each contrast individually. Each will produce ces and cesvar files. Take the difference between the ces files and the average of the cesvar files, then feed the result into mri_glmfit FFX
doug
On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote:
Hi Doug, I wanted to follow up on this. Would you be able to provide a workaround for contrasting multiple taskregs against each other? Is there something I can try in the meantime? Thanks, Caspar
2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik <cschwiedrz@rockefeller.edu mailto:cschwiedrz@rockefeller.edu>:
Hi Doug, thanks for your reply. I would like to feed the differences into a FFX group analysis, so I think I will need to resort to your workaround. It would be great if you could provide that. Thanks! Caspar 2014-11-10 13:45 GMT-05:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: To get sig maps for an individual, this is problematic but I could probably come up with a work-around. For a group analysis, you can simply compute each taskreg separately, then subtract the two prior to running mri_glmfit. doug On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote: > Hi! > A quick follow-up: > I have a taskreg file with 6 continuous predictors. I would like to > run specific contrasts, e.g., predictor 1 vs. mean(predictor 2:6). > From what I gather, selxavg3-sess will run automatic contrasts on > taskregs, but the automatic contrasts are against baseline. This is > not what I need at this point. > mk-contrast-sess does not like what I am putting in because I do not > have a paradigm file in which condition numbers are specified. > Is there a way to compute specific contrasts between multiple > taskregs, and if not, is there a workaround? > Thank you very much, Caspar > > > 2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik > <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>: > > Hi! > I have several external regressors in my analysis that I configure > with -taskreg in mkanalysis-sess (something like -notask -taskreg > nameoffile 6). > I was wondering how to set up mkcontrast-sess to contrast these > regerssors given that I do not have a paradigm file for them. > Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5? > > Thanks, Caspar > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
12:58 p.m.
ok, I will try that. How do I get the degrees of freedom? Thanks! Caspar
2014-11-11 12:04 GMT-05:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
Actually, you can still do each contrast individually. Each will produce ces and cesvar files. Take the difference between the ces files and the average of the cesvar files, then feed the result into mri_glmfit FFX
doug
On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote:
Hi Doug, I wanted to follow up on this. Would you be able to provide a workaround for contrasting multiple taskregs against each other? Is there something I can try in the meantime? Thanks, Caspar
2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik <cschwiedrz@rockefeller.edu mailto:cschwiedrz@rockefeller.edu>:
Hi Doug, thanks for your reply. I would like to feed the differences into a FFX group analysis, so I think I will need to resort to your workaround. It would be great if you could provide that. Thanks! Caspar 2014-11-10 13:45 GMT-05:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: To get sig maps for an individual, this is problematic but I could probably come up with a work-around. For a group analysis, youcan
simply compute each taskreg separately, then subtract the two prior to running mri_glmfit. doug On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote: > Hi! > A quick follow-up: > I have a taskreg file with 6 continuous predictors. I would like to > run specific contrasts, e.g., predictor 1 vs. mean(predictor 2:6). > From what I gather, selxavg3-sess will run automatic contrasts on > taskregs, but the automatic contrasts are against baseline. This is > not what I need at this point. > mk-contrast-sess does not like what I am putting in because I do not > have a paradigm file in which condition numbers are specified. > Is there a way to compute specific contrasts between multiple > taskregs, and if not, is there a workaround? > Thank you very much, Caspar > > > 2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik > <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>: > > Hi! > I have several external regressors in my analysis that I configure > with -taskreg in mkanalysis-sess (something like -notask -taskreg > nameoffile 6). > I was wondering how to set up mkcontrast-sess to contrast these > regerssors given that I do not have a paradigm file for them. > Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5? > > Thanks, Caspar > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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1:04 p.m.
It will be the same as the DOF of the individual contrasts (don't sum them).
On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote:
ok, I will try that. How do I get the degrees of freedom? Thanks! Caspar
2014-11-11 12:04 GMT-05:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
Actually, you can still do each contrast individually. Each will produce ces and cesvar files. Take the difference between the ces files and the average of the cesvar files, then feed the result into mri_glmfit FFX doug On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote: > Hi Doug, > I wanted to follow up on this. Would you be able to provide a > workaround for contrasting multiple taskregs against each other? Is > there something I can try in the meantime? Thanks, Caspar > > > 2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik > <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>: > > Hi Doug, > thanks for your reply. I would like to feed the differences into a > FFX group analysis, so I think I will need to resort to your > workaround. It would be great if you could provide that. Thanks! > Caspar > > 2014-11-10 13:45 GMT-05:00 Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>: > > > To get sig maps for an individual, this is problematic but I > could > probably come up with a work-around. For a group analysis, you can > simply compute each taskreg separately, then subtract the two > prior to > running mri_glmfit. > doug > > On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote: > > Hi! > > A quick follow-up: > > I have a taskreg file with 6 continuous predictors. I would > like to > > run specific contrasts, e.g., predictor 1 vs. mean(predictor > 2:6). > > From what I gather, selxavg3-sess will run automatic > contrasts on > > taskregs, but the automatic contrasts are against baseline. > This is > > not what I need at this point. > > mk-contrast-sess does not like what I am putting in because > I do not > > have a paradigm file in which condition numbers are specified. > > Is there a way to compute specific contrasts between multiple > > taskregs, and if not, is there a workaround? > > Thank you very much, Caspar > > > > > > 2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik > > <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>>: > > > > Hi! > > I have several external regressors in my analysis that I > configure > > with -taskreg in mkanalysis-sess (something like -notask > -taskreg > > nameoffile 6). > > I was wondering how to set up mkcontrast-sess to > contrast these > > regerssors given that I do not have a paradigm file for > them. > > Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5? > > > > Thanks, Caspar > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person > to whom it is > addressed. If you believe this e-mail was sent to you in error > and the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was > sent to you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
1:09 p.m.
I'll start the process thursday. On 11/11/2014 12:04 PM, Douglas N Greve wrote:
It will be the same as the DOF of the individual contrasts (don't sum them).
On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote:
ok, I will try that. How do I get the degrees of freedom? Thanks! Caspar
2014-11-11 12:04 GMT-05:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
Actually, you can still do each contrast individually. Each will produce ces and cesvar files. Take the difference between the ces files and the average of the cesvar files, then feed the result into mri_glmfit FFX doug On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote: > Hi Doug, > I wanted to follow up on this. Would you be able to provide a > workaround for contrasting multiple taskregs against each other? Is > there something I can try in the meantime? Thanks, Caspar > > > 2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik > <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>: > > Hi Doug, > thanks for your reply. I would like to feed the differences into a > FFX group analysis, so I think I will need to resort to your > workaround. It would be great if you could provide that. Thanks! > Caspar > > 2014-11-10 13:45 GMT-05:00 Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>: > > > To get sig maps for an individual, this is problematic but I > could > probably come up with a work-around. For a group analysis, you can > simply compute each taskreg separately, then subtract the two > prior to > running mri_glmfit. > doug > > On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote: > > Hi! > > A quick follow-up: > > I have a taskreg file with 6 continuous predictors. I would > like to > > run specific contrasts, e.g., predictor 1 vs. mean(predictor > 2:6). > > From what I gather, selxavg3-sess will run automatic > contrasts on > > taskregs, but the automatic contrasts are against baseline. > This is > > not what I need at this point. > > mk-contrast-sess does not like what I am putting in because > I do not > > have a paradigm file in which condition numbers are specified. > > Is there a way to compute specific contrasts between multiple > > taskregs, and if not, is there a workaround? > > Thank you very much, Caspar > > > > > > 2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik > > <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>>: > > > > Hi! > > I have several external regressors in my analysis that I > configure > > with -taskreg in mkanalysis-sess (something like -notask > -taskreg > > nameoffile 6). > > I was wondering how to set up mkcontrast-sess to > contrast these > > regerssors given that I do not have a paradigm file for > them. > > Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5? > > > > Thanks, Caspar > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person > to whom it is > addressed. If you believe this e-mail was sent to you in error > and the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was > sent to you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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1:19 p.m.
Sorry, Though we do have freesurfer pipelines we run in Madison, I responded to wrong email.
Bill Taylor Center for High Throughput Computing Computer Sciences University of Wisconsin, Madison
On 11/11/2014 12:09 PM, Bill Taylor wrote:
I'll start the process thursday. On 11/11/2014 12:04 PM, Douglas N Greve wrote:
It will be the same as the DOF of the individual contrasts (don't sum them).
On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote:
ok, I will try that. How do I get the degrees of freedom? Thanks! Caspar
2014-11-11 12:04 GMT-05:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
Actually, you can still do each contrast individually. Each will produce ces and cesvar files. Take the difference between the ces files and the average of the cesvar files, then feed the result into mri_glmfit FFX doug On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote: > Hi Doug, > I wanted to follow up on this. Would you be able to provide a > workaround for contrasting multiple taskregs against each other? Is > there something I can try in the meantime? Thanks, Caspar > > > 2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik > <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>: > > Hi Doug, > thanks for your reply. I would like to feed the differences into a > FFX group analysis, so I think I will need to resort to your > workaround. It would be great if you could provide that. Thanks! > Caspar > > 2014-11-10 13:45 GMT-05:00 Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>: > > > To get sig maps for an individual, this is problematic but I > could > probably come up with a work-around. For a group analysis, you can > simply compute each taskreg separately, then subtract the two > prior to > running mri_glmfit. > doug > > On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote: > > Hi! > > A quick follow-up: > > I have a taskreg file with 6 continuous predictors. I would > like to > > run specific contrasts, e.g., predictor 1 vs. mean(predictor > 2:6). > > From what I gather, selxavg3-sess will run automatic > contrasts on > > taskregs, but the automatic contrasts are against baseline. > This is > > not what I need at this point. > > mk-contrast-sess does not like what I am putting in because > I do not > > have a paradigm file in which condition numbers are specified. > > Is there a way to compute specific contrasts between multiple > > taskregs, and if not, is there a workaround? > > Thank you very much, Caspar > > > > > > 2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik > > <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>>: > > > > Hi! > > I have several external regressors in my analysis that I > configure > > with -taskreg in mkanalysis-sess (something like -notask > -taskreg > > nameoffile 6). > > I was wondering how to set up mkcontrast-sess to > contrast these > > regerssors given that I do not have a paradigm file for > them. > > Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5? > > > > Thanks, Caspar > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person > to whom it is > addressed. If you believe this e-mail was sent to you in error > and the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was > sent to you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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1:28 p.m.
Hi Doug, just to clarify: If I want to contrast taskreg 1 vs. mean(taskreg 2,3,4,5,6), I would compute ces= ces(taskreg 1) - mean(ces(taskreg 2,3,4,5,6)) and cesvar=mean(cesvar(taskreg(1,2,3,4,5,6)))
Is that correct? Thanks, Caspar
2014-11-11 13:19 GMT-05:00 Bill Taylor bt@cs.wisc.edu:
Sorry, Though we do have freesurfer pipelines we run in Madison, I responded to wrong email.
Bill Taylor Center for High Throughput Computing Computer Sciences University of Wisconsin, Madison
On 11/11/2014 12:09 PM, Bill Taylor wrote:
I'll start the process thursday. On 11/11/2014 12:04 PM, Douglas N Greve wrote:
It will be the same as the DOF of the individual contrasts (don't sum
them).
On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote:
ok, I will try that. How do I get the degrees of freedom? Thanks!
Caspar
2014-11-11 12:04 GMT-05:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
Actually, you can still do each contrast individually. Each will produce ces and cesvar files. Take the difference between the ces files and the average of the cesvar files, then feed the result intomri_glmfit FFX
doug On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote: > Hi Doug, > I wanted to follow up on this. Would you be able to provide a > workaround for contrasting multiple taskregs against eachother? Is
> there something I can try in the meantime? Thanks, Caspar > > > 2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik > <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu<mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>: > > Hi Doug, > thanks for your reply. I would like to feed the differences into a > FFX group analysis, so I think I will need to resort toyour
> workaround. It would be great if you could provide that.Thanks!
> Caspar > > 2014-11-10 13:45 GMT-05:00 Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>: > > > To get sig maps for an individual, this is problematic but I > could > probably come up with a work-around. For a group analysis, you can > simply compute each taskreg separately, then subtract the two > prior to > running mri_glmfit. > doug > > On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote: > > Hi! > > A quick follow-up: > > I have a taskreg file with 6 continuous predictors. I would > like to > > run specific contrasts, e.g., predictor 1 vs. mean(predictor > 2:6). > > From what I gather, selxavg3-sess will run automatic > contrasts on > > taskregs, but the automatic contrasts are against baseline. > This is > > not what I need at this point. > > mk-contrast-sess does not like what I am putting in because > I do not > > have a paradigm file in which condition numbers are specified. > > Is there a way to compute specific contrasts between multiple > > taskregs, and if not, is there a workaround? > > Thank you very much, Caspar > > > > > > 2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik > > <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>>:
> > > > Hi! > > I have several external regressors in my analysis that I > configure > > with -taskreg in mkanalysis-sess (something like -notask > -taskreg > > nameoffile 6). > > I was wondering how to set up mkcontrast-sess to > contrast these > > regerssors given that I do not have a paradigm file for > them. > > Can I just do something like -a 1 -c 2 -c 3 -c 4-c 5?
> > > > Thanks, Caspar > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person > to whom it is > addressed. If you believe this e-mail was sent to youin
error > and the e-mail > contains patient information, please contact thePartners
> Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was > sent to you in error > but does not contain patient information, pleasecontact the
> sender and properly > dispose of the e-mail. > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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1:54 p.m.
yes On 11/11/2014 01:28 PM, Caspar M. Schwiedrzik wrote:
Hi Doug, just to clarify: If I want to contrast taskreg 1 vs. mean(taskreg 2,3,4,5,6), I would compute ces= ces(taskreg 1) - mean(ces(taskreg 2,3,4,5,6)) and cesvar=mean(cesvar(taskreg(1,2,3,4,5,6)))
Is that correct? Thanks, Caspar
2014-11-11 13:19 GMT-05:00 Bill Taylor <bt@cs.wisc.edu mailto:bt@cs.wisc.edu>:
Sorry, Though we do have freesurfer pipelines we run in Madison, I responded to wrong email. Bill Taylor Center for High Throughput Computing Computer Sciences University of Wisconsin, Madison On 11/11/2014 12:09 PM, Bill Taylor wrote: > I'll start the process thursday. > On 11/11/2014 12:04 PM, Douglas N Greve wrote: >> It will be the same as the DOF of the individual contrasts (don't sum them). >> >> On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote: >>> ok, I will try that. How do I get the degrees of freedom? Thanks! Caspar >>> >>> 2014-11-11 12:04 GMT-05:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>: >>> >>> >>> Actually, you can still do each contrast individually. Each will >>> produce >>> ces and cesvar files. Take the difference between the ces files >>> and the >>> average of the cesvar files, then feed the result into mri_glmfit FFX >>> >>> doug >>> >>> >>> On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote: >>> > Hi Doug, >>> > I wanted to follow up on this. Would you be able to provide a >>> > workaround for contrasting multiple taskregs against each other? Is >>> > there something I can try in the meantime? Thanks, Caspar >>> > >>> > >>> > 2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik >>> > <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>>: >>> > >>> > Hi Doug, >>> > thanks for your reply. I would like to feed the differences >>> into a >>> > FFX group analysis, so I think I will need to resort to your >>> > workaround. It would be great if you could provide that. Thanks! >>> > Caspar >>> > >>> > 2014-11-10 13:45 GMT-05:00 Douglas N Greve >>> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>: >>> > >>> > >>> > To get sig maps for an individual, this is problematic >>> but I >>> > could >>> > probably come up with a work-around. For a group >>> analysis, you can >>> > simply compute each taskreg separately, then subtract >>> the two >>> > prior to >>> > running mri_glmfit. >>> > doug >>> > >>> > On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote: >>> > > Hi! >>> > > A quick follow-up: >>> > > I have a taskreg file with 6 continuous predictors. I >>> would >>> > like to >>> > > run specific contrasts, e.g., predictor 1 vs. >>> mean(predictor >>> > 2:6). >>> > > From what I gather, selxavg3-sess will run automatic >>> > contrasts on >>> > > taskregs, but the automatic contrasts are against >>> baseline. >>> > This is >>> > > not what I need at this point. >>> > > mk-contrast-sess does not like what I am putting in >>> because >>> > I do not >>> > > have a paradigm file in which condition numbers are >>> specified. >>> > > Is there a way to compute specific contrasts between >>> multiple >>> > > taskregs, and if not, is there a workaround? >>> > > Thank you very much, Caspar >>> > > >>> > > >>> > > 2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik >>> > > <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> >>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>> >>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> >>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>>>: >>> > > >>> > > Hi! >>> > > I have several external regressors in my analysis >>> that I >>> > configure >>> > > with -taskreg in mkanalysis-sess (something like >>> -notask >>> > -taskreg >>> > > nameoffile 6). >>> > > I was wondering how to set up mkcontrast-sess to >>> > contrast these >>> > > regerssors given that I do not have a paradigm >>> file for >>> > them. >>> > > Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5? >>> > > >>> > > Thanks, Caspar >>> > > >>> > > >>> > > >>> > > >>> > > _______________________________________________ >>> > > Freesurfer mailing list >>> > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> >>> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> > >>> > -- >>> > Douglas N. Greve, Ph.D. >>> > MGH-NMR Center >>> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> >>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> >>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> >>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> >>> <tel:617-726-7422 <tel:617-726-7422>>> >>> > >>> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> > >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> > Outgoing: >>> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> > >>> > _______________________________________________ >>> > Freesurfer mailing list >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> > >>> > >>> > The information in this e-mail is intended only for the >>> person >>> > to whom it is >>> > addressed. If you believe this e-mail was sent to you in >>> error >>> > and the e-mail >>> > contains patient information, please contact the Partners >>> > Compliance HelpLine at >>> > http://www.partners.org/complianceline . If the e-mail was >>> > sent to you in error >>> > but does not contain patient information, please contact the >>> > sender and properly >>> > dispose of the e-mail. >>> > >>> > >>> > >>> > >>> > >>> > _______________________________________________ >>> > Freesurfer mailing list >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> >>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> Outgoing: >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
4:37 p.m.
Hi Doug, I am a little bit confused about the variance. Shouldn't the relevant variance be the variance over the differences, not the mean variance over all? Of course at the level of ces and cesvar, I do not have access to the timepoint by timepoint differences anymore. Is there another way to do this? Thanks, Caspar
2014-11-11 13:54 GMT-05:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
yes On 11/11/2014 01:28 PM, Caspar M. Schwiedrzik wrote:
Hi Doug, just to clarify: If I want to contrast taskreg 1 vs. mean(taskreg 2,3,4,5,6), I would compute ces= ces(taskreg 1) - mean(ces(taskreg 2,3,4,5,6)) and cesvar=mean(cesvar(taskreg(1,2,3,4,5,6)))
Is that correct? Thanks, Caspar
2014-11-11 13:19 GMT-05:00 Bill Taylor <bt@cs.wisc.edu mailto:bt@cs.wisc.edu>:
Sorry, Though we do have freesurfer pipelines we run in Madison, I responded to wrong email. Bill Taylor Center for High Throughput Computing Computer Sciences University of Wisconsin, Madison On 11/11/2014 12:09 PM, Bill Taylor wrote: > I'll start the process thursday. > On 11/11/2014 12:04 PM, Douglas N Greve wrote: >> It will be the same as the DOF of the individual contrasts (don't sum them). >> >> On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote: >>> ok, I will try that. How do I get the degrees of freedom? Thanks! Caspar >>> >>> 2014-11-11 12:04 GMT-05:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>: >>> >>> >>> Actually, you can still do each contrast individually. Each will >>> produce >>> ces and cesvar files. Take the difference between the ces files >>> and the >>> average of the cesvar files, then feed the result into mri_glmfit FFX >>> >>> doug >>> >>> >>> On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote: >>> > Hi Doug, >>> > I wanted to follow up on this. Would you be able to provide a >>> > workaround for contrasting multiple taskregs against each other? Is >>> > there something I can try in the meantime? Thanks, Caspar >>> > >>> > >>> > 2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik >>> > <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>>: >>> > >>> > Hi Doug, >>> > thanks for your reply. I would like to feed the differences >>> into a >>> > FFX group analysis, so I think I will need to resort to your >>> > workaround. It would be great if you could provide that. Thanks! >>> > Caspar >>> > >>> > 2014-11-10 13:45 GMT-05:00 Douglas N Greve >>> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>: >>> > >>> > >>> > To get sig maps for an individual, this is problematic >>> but I >>> > could >>> > probably come up with a work-around. For a group >>> analysis, you can >>> > simply compute each taskreg separately, then subtract >>> the two >>> > prior to >>> > running mri_glmfit. >>> > doug >>> > >>> > On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote: >>> > > Hi! >>> > > A quick follow-up: >>> > > I have a taskreg file with 6 continuous predictors. I >>> would >>> > like to >>> > > run specific contrasts, e.g., predictor 1 vs. >>> mean(predictor >>> > 2:6). >>> > > From what I gather, selxavg3-sess will run automatic >>> > contrasts on >>> > > taskregs, but the automatic contrasts are against >>> baseline. >>> > This is >>> > > not what I need at this point. >>> > > mk-contrast-sess does not like what I am putting in >>> because >>> > I do not >>> > > have a paradigm file in which condition numbers are >>> specified. >>> > > Is there a way to compute specific contrasts between >>> multiple >>> > > taskregs, and if not, is there a workaround? >>> > > Thank you very much, Caspar >>> > > >>> > > >>> > > 2014-11-06 15:23 GMT-05:00 Caspar M.Schwiedrzik
>>> > > <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> >>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>> >>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> >>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>>>: >>> > > >>> > > Hi! >>> > > I have several external regressors in my analysis >>> that I >>> > configure >>> > > with -taskreg in mkanalysis-sess (something like >>> -notask >>> > -taskreg >>> > > nameoffile 6). >>> > > I was wondering how to set up mkcontrast-sess to >>> > contrast these >>> > > regerssors given that I do not have a paradigm >>> file for >>> > them. >>> > > Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5? >>> > > >>> > > Thanks, Caspar >>> > > >>> > > >>> > > >>> > > >>> > > _______________________________________________ >>> > > Freesurfer mailing list >>> > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> >>> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> > >>> > -- >>> > Douglas N. Greve, Ph.D. >>> > MGH-NMR Center >>> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> >>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> >>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> >>> <tel:617-726-7422 <tel:617-726-7422>>> >>> > >>> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> > >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> > Outgoing: >>> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> > >>> > _______________________________________________ >>> > Freesurfer mailing list >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> > >>> > >>> > The information in this e-mail is intended only for the >>> person >>> > to whom it is >>> > addressed. If you believe this e-mail was sent to you in >>> error >>> > and the e-mail >>> > contains patient information, please contact the Partners >>> > Compliance HelpLine at >>> > http://www.partners.org/complianceline . If the e-mailwas
>>> > sent to you in error >>> > but does not contain patient information, please contact the >>> > sender and properly >>> > dispose of the e-mail. >>> > >>> > >>> > >>> > >>> > >>> > _______________________________________________ >>> > Freesurfer mailing list >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> >>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> Outgoing: >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
13 Nov
13 Nov
10:18 a.m.
Hi Doug, coming back to this once more. I am thinking that I can bypass mkcontrast-sess entirely if I provide a contrast matrix that has ContrastMtx_0 and WCond set to the contrast that I am interested in. For example [1 -0.2 -0.2 -0.2 -0.2 -0.2] to contrast my first continuous predictor and against the remaining five continuous predictors. For that, I would just place a corresponding mat file in a subdirectory in mystudy. Is there anything that speaks that and anything else that I need to consider? Thanks! Caspar
2014-11-11 16:37 GMT-05:00 Caspar M. Schwiedrzik <cschwiedrz@rockefeller.edu
:
Hi Doug, I am a little bit confused about the variance. Shouldn't the relevant variance be the variance over the differences, not the mean variance over all? Of course at the level of ces and cesvar, I do not have access to the timepoint by timepoint differences anymore. Is there another way to do this? Thanks, Caspar
2014-11-11 13:54 GMT-05:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
yes
On 11/11/2014 01:28 PM, Caspar M. Schwiedrzik wrote:
Hi Doug, just to clarify: If I want to contrast taskreg 1 vs. mean(taskreg 2,3,4,5,6), I would compute ces= ces(taskreg 1) - mean(ces(taskreg 2,3,4,5,6)) and cesvar=mean(cesvar(taskreg(1,2,3,4,5,6)))
Is that correct? Thanks, Caspar
2014-11-11 13:19 GMT-05:00 Bill Taylor <bt@cs.wisc.edu mailto:bt@cs.wisc.edu>:
Sorry, Though we do have freesurfer pipelines we run in Madison, I responded to wrong email. Bill Taylor Center for High Throughput Computing Computer Sciences University of Wisconsin, Madison On 11/11/2014 12:09 PM, Bill Taylor wrote: > I'll start the process thursday. > On 11/11/2014 12:04 PM, Douglas N Greve wrote: >> It will be the same as the DOF of the individual contrasts (don't sum them). >> >> On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote: >>> ok, I will try that. How do I get the degrees of freedom? Thanks! Caspar >>> >>> 2014-11-11 12:04 GMT-05:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>: >>> >>> >>> Actually, you can still do each contrast individually. Each will >>> produce >>> ces and cesvar files. Take the difference between the ces files >>> and the >>> average of the cesvar files, then feed the result into mri_glmfit FFX >>> >>> doug >>> >>> >>> On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote: >>> > Hi Doug, >>> > I wanted to follow up on this. Would you be able to provide a >>> > workaround for contrasting multiple taskregs against each other? Is >>> > there something I can try in the meantime? Thanks,Caspar
>>> > >>> > >>> > 2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik >>> > <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>>: >>> > >>> > Hi Doug, >>> > thanks for your reply. I would like to feed the differences >>> into a >>> > FFX group analysis, so I think I will need to resort to your >>> > workaround. It would be great if you could provide that. Thanks! >>> > Caspar >>> > >>> > 2014-11-10 13:45 GMT-05:00 Douglas N Greve >>> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>: >>> > >>> > >>> > To get sig maps for an individual, this is problematic >>> but I >>> > could >>> > probably come up with a work-around. For a group >>> analysis, you can >>> > simply compute each taskreg separately, then subtract >>> the two >>> > prior to >>> > running mri_glmfit. >>> > doug >>> > >>> > On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote: >>> > > Hi! >>> > > A quick follow-up: >>> > > I have a taskreg file with 6 continuous predictors. I >>> would >>> > like to >>> > > run specific contrasts, e.g., predictor 1 vs. >>> mean(predictor >>> > 2:6). >>> > > From what I gather, selxavg3-sess will run automatic >>> > contrasts on >>> > > taskregs, but the automatic contrasts are against >>> baseline. >>> > This is >>> > > not what I need at this point. >>> > > mk-contrast-sess does not like what I am putting in >>> because >>> > I do not >>> > > have a paradigm file in which condition numbers are >>> specified. >>> > > Is there a way to compute specific contrasts between >>> multiple >>> > > taskregs, and if not, is there a workaround? >>> > > Thank you very much, Caspar >>> > > >>> > > >>> > > 2014-11-06 15:23 GMT-05:00 Caspar M.Schwiedrzik
>>> > > <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> >>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>> >>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> >>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>>>: >>> > > >>> > > Hi! >>> > > I have several external regressors in my analysis >>> that I >>> > configure >>> > > with -taskreg in mkanalysis-sess (something like >>> -notask >>> > -taskreg >>> > > nameoffile 6). >>> > > I was wondering how to set up mkcontrast-sess to >>> > contrast these >>> > > regerssors given that I do not have a paradigm >>> file for >>> > them. >>> > > Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5? >>> > > >>> > > Thanks, Caspar >>> > > >>> > > >>> > > >>> > > >>> > >
>>> > > Freesurfer mailing list >>> > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> >>> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> > >>> > -- >>> > Douglas N. Greve, Ph.D. >>> > MGH-NMR Center >>> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> >>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> >>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> >>> <tel:617-726-7422 <tel:617-726-7422>>> >>> > >>> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> > >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> > Outgoing: >>> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> > >>> > _______________________________________________ >>> > Freesurfer mailing list >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> > >>> > >>> > The information in this e-mail is intended only for the >>> person >>> > to whom it is >>> > addressed. If you believe this e-mail was sent to you in >>> error >>> > and the e-mail >>> > contains patient information, please contact the Partners >>> > Compliance HelpLine at >>> > http://www.partners.org/complianceline . If the e-mailwas
>>> > sent to you in error >>> > but does not contain patient information, please contact the >>> > sender and properly >>> > dispose of the e-mail. >>> > >>> > >>> > >>> > >>> > >>> > _______________________________________________ >>> > Freesurfer mailing list >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> >>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> Outgoing: >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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12:16 p.m.
I don't know whether that will work or not. If it runs, you can compare the result to computing the contrast manually to see if there is a difference. If there is no difference, then it works.
On 11/13/2014 10:18 AM, Caspar M. Schwiedrzik wrote:
Hi Doug, coming back to this once more. I am thinking that I can bypass mkcontrast-sess entirely if I provide a contrast matrix that has ContrastMtx_0 and WCond set to the contrast that I am interested in. For example [1 -0.2 -0.2 -0.2 -0.2 -0.2] to contrast my first continuous predictor and against the remaining five continuous predictors. For that, I would just place a corresponding mat file in a subdirectory in mystudy. Is there anything that speaks that and anything else that I need to consider? Thanks! Caspar
2014-11-11 16:37 GMT-05:00 Caspar M. Schwiedrzik <cschwiedrz@rockefeller.edu mailto:cschwiedrz@rockefeller.edu>:
Hi Doug, I am a little bit confused about the variance. Shouldn't the relevant variance be the variance over the differences, not the mean variance over all? Of course at the level of ces and cesvar, I do not have access to the timepoint by timepoint differences anymore. Is there another way to do this? Thanks, Caspar 2014-11-11 13:54 GMT-05:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: yes On 11/11/2014 01:28 PM, Caspar M. Schwiedrzik wrote: > Hi Doug, > just to clarify: > If I want to contrast taskreg 1 vs. mean(taskreg 2,3,4,5,6), I would > compute > ces= ces(taskreg 1) - mean(ces(taskreg 2,3,4,5,6)) > and > cesvar=mean(cesvar(taskreg(1,2,3,4,5,6))) > > Is that correct? > Thanks, Caspar > > > 2014-11-11 13:19 GMT-05:00 Bill Taylor <bt@cs.wisc.edu <mailto:bt@cs.wisc.edu> > <mailto:bt@cs.wisc.edu <mailto:bt@cs.wisc.edu>>>: > > Sorry, Though we do have freesurfer pipelines we run in Madison, I > responded to wrong email. > > Bill Taylor > Center for High Throughput Computing > Computer Sciences > University of Wisconsin, Madison > > On 11/11/2014 12:09 PM, Bill Taylor wrote: > > I'll start the process thursday. > > On 11/11/2014 12:04 PM, Douglas N Greve wrote: > >> It will be the same as the DOF of the individual contrasts > (don't sum them). > >> > >> On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote: > >>> ok, I will try that. How do I get the degrees of freedom? > Thanks! Caspar > >>> > >>> 2014-11-11 12:04 GMT-05:00 Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>: > >>> > >>> > >>> Actually, you can still do each contrast individually. > Each will > >>> produce > >>> ces and cesvar files. Take the difference between the > ces files > >>> and the > >>> average of the cesvar files, then feed the result into > mri_glmfit FFX > >>> > >>> doug > >>> > >>> > >>> On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote: > >>> > Hi Doug, > >>> > I wanted to follow up on this. Would you be able to > provide a > >>> > workaround for contrasting multiple taskregs against > each other? Is > >>> > there something I can try in the meantime? Thanks, Caspar > >>> > > >>> > > >>> > 2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik > >>> > <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>> > >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>>>: > >>> > > >>> > Hi Doug, > >>> > thanks for your reply. I would like to feed the > differences > >>> into a > >>> > FFX group analysis, so I think I will need to > resort to your > >>> > workaround. It would be great if you could provide > that. Thanks! > >>> > Caspar > >>> > > >>> > 2014-11-10 13:45 GMT-05:00 Douglas N Greve > >>> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>>: > >>> > > >>> > > >>> > To get sig maps for an individual, this is > problematic > >>> but I > >>> > could > >>> > probably come up with a work-around. For a group > >>> analysis, you can > >>> > simply compute each taskreg separately, then > subtract > >>> the two > >>> > prior to > >>> > running mri_glmfit. > >>> > doug > >>> > > >>> > On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik > wrote: > >>> > > Hi! > >>> > > A quick follow-up: > >>> > > I have a taskreg file with 6 continuous > predictors. I > >>> would > >>> > like to > >>> > > run specific contrasts, e.g., predictor 1 vs. > >>> mean(predictor > >>> > 2:6). > >>> > > From what I gather, selxavg3-sess will run > automatic > >>> > contrasts on > >>> > > taskregs, but the automatic contrasts are > against > >>> baseline. > >>> > This is > >>> > > not what I need at this point. > >>> > > mk-contrast-sess does not like what I am > putting in > >>> because > >>> > I do not > >>> > > have a paradigm file in which condition > numbers are > >>> specified. > >>> > > Is there a way to compute specific contrasts > between > >>> multiple > >>> > > taskregs, and if not, is there a workaround? > >>> > > Thank you very much, Caspar > >>> > > > >>> > > > >>> > > 2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik > >>> > > <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>> > >>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>> > >>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>> > >>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>>>>: > >>> > > > >>> > > Hi! > >>> > > I have several external regressors in my > analysis > >>> that I > >>> > configure > >>> > > with -taskreg in mkanalysis-sess > (something like > >>> -notask > >>> > -taskreg > >>> > > nameoffile 6). > >>> > > I was wondering how to set up > mkcontrast-sess to > >>> > contrast these > >>> > > regerssors given that I do not have a > paradigm > >>> file for > >>> > them. > >>> > > Can I just do something like -a 1 -c 2 > -c 3 -c 4 -c 5? > >>> > > > >>> > > Thanks, Caspar > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > _______________________________________________ > >>> > > Freesurfer mailing list > >>> > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > >>> > > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > > >>> > -- > >>> > Douglas N. Greve, Ph.D. > >>> > MGH-NMR Center > >>> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > >>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > >>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>>> > >>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > >>> <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>>> > >>> > > >>> > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >>> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >>> > FileDrop: > https://gate.nmr.mgh.harvard.edu/filedrop2 > >>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >>> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >>> > > >>> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >>> > Outgoing: > >>> > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >>> > > >>> > _______________________________________________ > >>> > Freesurfer mailing list > >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > >>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > > >>> > > >>> > The information in this e-mail is intended > only for the > >>> person > >>> > to whom it is > >>> > addressed. If you believe this e-mail was sent > to you in > >>> error > >>> > and the e-mail > >>> > contains patient information, please contact > the Partners > >>> > Compliance HelpLine at > >>> > http://www.partners.org/complianceline . If the e-mail was > >>> > sent to you in error > >>> > but does not contain patient information, > please contact the > >>> > sender and properly > >>> > dispose of the e-mail. > >>> > > >>> > > >>> > > >>> > > >>> > > >>> > _______________________________________________ > >>> > Freesurfer mailing list > >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> -- > >>> Douglas N. Greve, Ph.D. > >>> MGH-NMR Center > >>> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > >>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > >>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > >>> > >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >>> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >>> Outgoing: > >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
5:33 p.m.
Hi Doug, so I made contrast matrices and stored them in mystudy, and then ran selxavg3-sess per subject. I defined three different contrasts (in three mat files), but selxacg3-sess only gives me one analysis, it seems to be an F-test. When I do isxconcat-sess after that, I get six ces files per analysis (I presume one for each of my predictors), not three (number of contrasts).
Is there a way for me to force selxavg3-sess to actually compute the contrasts that I want?
Thanks, Caspar
2014-11-13 12:16 GMT-05:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
I don't know whether that will work or not. If it runs, you can compare the result to computing the contrast manually to see if there is a difference. If there is no difference, then it works.
On 11/13/2014 10:18 AM, Caspar M. Schwiedrzik wrote:
Hi Doug, coming back to this once more. I am thinking that I can bypass mkcontrast-sess entirely if I provide a contrast matrix that has ContrastMtx_0 and WCond set to the contrast that I am interested in. For example [1 -0.2 -0.2 -0.2 -0.2 -0.2] to contrast my first continuous predictor and against the remaining five continuous predictors. For that, I would just place a corresponding mat file in a subdirectory in mystudy. Is there anything that speaks that and anything else that I need to consider? Thanks! Caspar
2014-11-11 16:37 GMT-05:00 Caspar M. Schwiedrzik <cschwiedrz@rockefeller.edu mailto:cschwiedrz@rockefeller.edu>:
Hi Doug, I am a little bit confused about the variance. Shouldn't the relevant variance be the variance over the differences, not the mean variance over all? Of course at the level of ces and cesvar, I do not have access to the timepoint by timepoint differences anymore. Is there another way to do this? Thanks, Caspar 2014-11-11 13:54 GMT-05:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: yes On 11/11/2014 01:28 PM, Caspar M. Schwiedrzik wrote: > Hi Doug, > just to clarify: > If I want to contrast taskreg 1 vs. mean(taskreg 2,3,4,5,6), I would > compute > ces= ces(taskreg 1) - mean(ces(taskreg 2,3,4,5,6)) > and > cesvar=mean(cesvar(taskreg(1,2,3,4,5,6))) > > Is that correct? > Thanks, Caspar > > > 2014-11-11 13:19 GMT-05:00 Bill Taylor <bt@cs.wisc.edu <mailto:bt@cs.wisc.edu> > <mailto:bt@cs.wisc.edu <mailto:bt@cs.wisc.edu>>>: > > Sorry, Though we do have freesurfer pipelines we run in Madison, I > responded to wrong email. > > Bill Taylor > Center for High Throughput Computing > Computer Sciences > University of Wisconsin, Madison > > On 11/11/2014 12:09 PM, Bill Taylor wrote: > > I'll start the process thursday. > > On 11/11/2014 12:04 PM, Douglas N Greve wrote: > >> It will be the same as the DOF of the individual contrasts > (don't sum them). > >> > >> On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote: > >>> ok, I will try that. How do I get the degrees of freedom? > Thanks! Caspar > >>> > >>> 2014-11-11 12:04 GMT-05:00 Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>:
> >>> > >>> > >>> Actually, you can still do each contrast individually. > Each will > >>> produce > >>> ces and cesvar files. Take the difference between the > ces files > >>> and the > >>> average of the cesvar files, then feed the result into > mri_glmfit FFX > >>> > >>> doug > >>> > >>> > >>> On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote: > >>> > Hi Doug, > >>> > I wanted to follow up on this. Would you be able to > provide a > >>> > workaround for contrasting multiple taskregs against > each other? Is > >>> > there something I can try in the meantime? Thanks, Caspar > >>> > > >>> > > >>> > 2014-11-10 13:54 GMT-05:00 Caspar M.Schwiedrzik
> >>> > <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>> > >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>>>: > >>> > > >>> > Hi Doug, > >>> > thanks for your reply. I would like to feed the > differences > >>> into a > >>> > FFX group analysis, so I think I will need to > resort to your > >>> > workaround. It would be great if you could provide > that. Thanks! > >>> > Caspar > >>> > > >>> > 2014-11-10 13:45 GMT-05:00 Douglas N Greve > >>> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>>: > >>> > > >>> > > >>> > To get sig maps for an individual, this is > problematic > >>> but I > >>> > could > >>> > probably come up with a work-around. For a group > >>> analysis, you can > >>> > simply compute each taskreg separately, then > subtract > >>> the two > >>> > prior to > >>> > running mri_glmfit. > >>> > doug > >>> > > >>> > On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik > wrote: > >>> > > Hi! > >>> > > A quick follow-up: > >>> > > I have a taskreg file with 6 continuous > predictors. I > >>> would > >>> > like to > >>> > > run specific contrasts, e.g., predictor 1 vs. > >>> mean(predictor > >>> > 2:6). > >>> > > From what I gather, selxavg3-sess will run > automatic > >>> > contrasts on > >>> > > taskregs, but the automatic contrasts are > against > >>> baseline. > >>> > This is > >>> > > not what I need at this point. > >>> > > mk-contrast-sess does not like what I am > putting in > >>> because > >>> > I do not > >>> > > have a paradigm file in which condition > numbers are > >>> specified. > >>> > > Is there a way to compute specific contrasts > between > >>> multiple > >>> > > taskregs, and if not, is there a workaround? > >>> > > Thank you very much, Caspar > >>> > > > >>> > > > >>> > > 2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik > >>> > > <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>> > >>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>> > >>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>> > >>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>>>>: > >>> > > > >>> > > Hi! > >>> > > I have several external regressors in my > analysis > >>> that I > >>> > configure > >>> > > with -taskreg in mkanalysis-sess > (something like > >>> -notask > >>> > -taskreg > >>> > > nameoffile 6). > >>> > > I was wondering how to set up > mkcontrast-sess to > >>> > contrast these > >>> > > regerssors given that I do not have a > paradigm > >>> file for > >>> > them. > >>> > > Can I just do something like -a 1 -c 2 > -c 3 -c 4 -c 5? > >>> > > > >>> > > Thanks, Caspar > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > _______________________________________________ > >>> > > Freesurfer mailing list > >>> > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > >>> > > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > > >>> > -- > >>> > Douglas N. Greve, Ph.D. > >>> > MGH-NMR Center > >>> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > >>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > >>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>>> > >>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > >>> <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>>> > >>> > > >>> > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >>> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >>> > FileDrop: > https://gate.nmr.mgh.harvard.edu/filedrop2 > >>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >>> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >>> > > >>> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >>> > Outgoing: > >>> > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >>> > > >>> > _______________________________________________ > >>> > Freesurfer mailing list > >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > >>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > > >>> > > >>> > The information in this e-mail is intended > only for the > >>> person > >>> > to whom it is > >>> > addressed. If you believe this e-mail was sent > to you in > >>> error > >>> > and the e-mail > >>> > contains patient information, please contact > the Partners > >>> > Compliance HelpLine at > >>> > http://www.partners.org/complianceline . If the e-mail was > >>> > sent to you in error > >>> > but does not contain patient information, > please contact the > >>> > sender and properly > >>> > dispose of the e-mail. > >>> > > >>> > > >>> > > >>> > > >>> > > >>> > _______________________________________________ > >>> > Freesurfer mailing list > >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> -- > >>> Douglas N. Greve, Ph.D. > >>> MGH-NMR Center > >>> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > >>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > >>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > >>> > >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >>> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >>> Outgoing: > >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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6:42 p.m.
ok, so the issue is in fast_ldanaflac.m, around line 520: flac.con(nthcon).ContrastMtx_0=[]; that effectively ignores the contrasts that are set up in mystudy. caspar
2014-11-13 17:33 GMT-05:00 Caspar M. Schwiedrzik <cschwiedrz@rockefeller.edu
:
Hi Doug, so I made contrast matrices and stored them in mystudy, and then ran selxavg3-sess per subject. I defined three different contrasts (in three mat files), but selxacg3-sess only gives me one analysis, it seems to be an F-test. When I do isxconcat-sess after that, I get six ces files per analysis (I presume one for each of my predictors), not three (number of contrasts).
Is there a way for me to force selxavg3-sess to actually compute the contrasts that I want?
Thanks, Caspar
2014-11-13 12:16 GMT-05:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
I don't know whether that will work or not. If it runs, you can compare
the result to computing the contrast manually to see if there is a difference. If there is no difference, then it works.
On 11/13/2014 10:18 AM, Caspar M. Schwiedrzik wrote:
Hi Doug, coming back to this once more. I am thinking that I can bypass mkcontrast-sess entirely if I provide a contrast matrix that has ContrastMtx_0 and WCond set to the contrast that I am interested in. For example [1 -0.2 -0.2 -0.2 -0.2 -0.2] to contrast my first continuous predictor and against the remaining five continuous predictors. For that, I would just place a corresponding mat file in a subdirectory in mystudy. Is there anything that speaks that and anything else that I need to consider? Thanks! Caspar
2014-11-11 16:37 GMT-05:00 Caspar M. Schwiedrzik <cschwiedrz@rockefeller.edu mailto:cschwiedrz@rockefeller.edu>:
Hi Doug, I am a little bit confused about the variance. Shouldn't the relevant variance be the variance over the differences, not the mean variance over all? Of course at the level of ces and cesvar, I do not have access to the timepoint by timepoint differences anymore. Is there another way to do this? Thanks, Caspar 2014-11-11 13:54 GMT-05:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: yes On 11/11/2014 01:28 PM, Caspar M. Schwiedrzik wrote: > Hi Doug, > just to clarify: > If I want to contrast taskreg 1 vs. mean(taskreg 2,3,4,5,6), I would > compute > ces= ces(taskreg 1) - mean(ces(taskreg 2,3,4,5,6)) > and > cesvar=mean(cesvar(taskreg(1,2,3,4,5,6))) > > Is that correct? > Thanks, Caspar > > > 2014-11-11 13:19 GMT-05:00 Bill Taylor <bt@cs.wisc.edu <mailto:bt@cs.wisc.edu> > <mailto:bt@cs.wisc.edu <mailto:bt@cs.wisc.edu>>>: > > Sorry, Though we do have freesurfer pipelines we run in Madison, I > responded to wrong email. > > Bill Taylor > Center for High Throughput Computing > Computer Sciences > University of Wisconsin, Madison > > On 11/11/2014 12:09 PM, Bill Taylor wrote: > > I'll start the process thursday. > > On 11/11/2014 12:04 PM, Douglas N Greve wrote: > >> It will be the same as the DOF of the individual contrasts > (don't sum them). > >> > >> On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote: > >>> ok, I will try that. How do I get the degrees of freedom? > Thanks! Caspar > >>> > >>> 2014-11-11 12:04 GMT-05:00 Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>:
> >>> > >>> > >>> Actually, you can still do each contrast individually. > Each will > >>> produce > >>> ces and cesvar files. Take the difference between the > ces files > >>> and the > >>> average of the cesvar files, then feed the result into > mri_glmfit FFX > >>> > >>> doug > >>> > >>> > >>> On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote: > >>> > Hi Doug, > >>> > I wanted to follow up on this. Would you be able to > provide a > >>> > workaround for contrasting multiple taskregs against > each other? Is > >>> > there something I can try in the meantime? Thanks, Caspar > >>> > > >>> > > >>> > 2014-11-10 13:54 GMT-05:00 Caspar M.Schwiedrzik
> >>> > <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>> > >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>>>: > >>> > > >>> > Hi Doug, > >>> > thanks for your reply. I would like to feed the > differences > >>> into a > >>> > FFX group analysis, so I think I will need to > resort to your > >>> > workaround. It would be great if you could provide > that. Thanks! > >>> > Caspar > >>> > > >>> > 2014-11-10 13:45 GMT-05:00 Douglas N Greve > >>> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>>: > >>> > > >>> > > >>> > To get sig maps for an individual, this is > problematic > >>> but I > >>> > could > >>> > probably come up with a work-around. For a group > >>> analysis, you can > >>> > simply compute each taskreg separately, then > subtract > >>> the two > >>> > prior to > >>> > running mri_glmfit. > >>> > doug > >>> > > >>> > On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik > wrote: > >>> > > Hi! > >>> > > A quick follow-up: > >>> > > I have a taskreg file with 6 continuous > predictors. I > >>> would > >>> > like to > >>> > > run specific contrasts, e.g., predictor 1 vs. > >>> mean(predictor > >>> > 2:6). > >>> > > From what I gather, selxavg3-sess will run > automatic > >>> > contrasts on > >>> > > taskregs, but the automatic contrasts are > against > >>> baseline. > >>> > This is > >>> > > not what I need at this point. > >>> > > mk-contrast-sess does not like what I am > putting in > >>> because > >>> > I do not > >>> > > have a paradigm file in which condition > numbers are > >>> specified. > >>> > > Is there a way to compute specific contrasts > between > >>> multiple > >>> > > taskregs, and if not, is there a workaround? > >>> > > Thank you very much, Caspar > >>> > > > >>> > > > >>> > > 2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik > >>> > > <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>> > >>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>> > >>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>> > >>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>>>>: > >>> > > > >>> > > Hi! > >>> > > I have several external regressors in my > analysis > >>> that I > >>> > configure > >>> > > with -taskreg in mkanalysis-sess > (something like > >>> -notask > >>> > -taskreg > >>> > > nameoffile 6). > >>> > > I was wondering how to set up > mkcontrast-sess to > >>> > contrast these > >>> > > regerssors given that I do not have a > paradigm > >>> file for > >>> > them. > >>> > > Can I just do something like -a 1 -c 2 > -c 3 -c 4 -c 5? > >>> > > > >>> > > Thanks, Caspar > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > _______________________________________________ > >>> > > Freesurfer mailing list > >>> > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > >>> > > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > > >>> > -- > >>> > Douglas N. Greve, Ph.D. > >>> > MGH-NMR Center > >>> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > >>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > >>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>>> > >>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > >>> <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>>> > >>> > > >>> > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >>> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >>> > FileDrop: > https://gate.nmr.mgh.harvard.edu/filedrop2 > >>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >>> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >>> > > >>> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >>> > Outgoing: > >>> > >ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >>> > > >>> >
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> to you in > >>> error > >>> > and the e-mail > >>> > contains patient information, please contact > the Partners > >>> > Compliance HelpLine at > >>> > http://www.partners.org/complianceline . If the e-mail was > >>> > sent to you in error > >>> > but does not contain patient information, > please contact the > >>> > sender and properly > >>> > dispose of the e-mail. > >>> > > >>> > > >>> > > >>> > > >>> > > >>> >
> >>> > Freesurfer mailing list > >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> -- > >>> Douglas N. Greve, Ph.D. > >>> MGH-NMR Center > >>> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > >>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > >>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > >>> > >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >>> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >>> Outgoing: > >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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17 Nov
17 Nov
12:38 p.m.
That is what I thought. For version 6, I have a work-around which you might be able to use with version 5. Copy these files
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_ldanaflac.m ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/flac_conmat.m
to $FREESURFER_HOME/fsfast/toolbox (make backups of the ones that are already there).
Then create a file for your contrast in the folder created by mkanalysis-sess (eg, yourcontrast.mtx). Note the mtx ending and not .mat ending. This is a text file with the contrast that you want. I would suggest making a contrast that replicates one of the other contrasts you made with mkcontrast-sess to assure that you have it right.
doug
On 11/13/2014 06:42 PM, Caspar M. Schwiedrzik wrote:
ok, so the issue is in fast_ldanaflac.m, around line 520: flac.con(nthcon).ContrastMtx_0=[]; that effectively ignores the contrasts that are set up in mystudy. caspar
2014-11-13 17:33 GMT-05:00 Caspar M. Schwiedrzik <cschwiedrz@rockefeller.edu mailto:cschwiedrz@rockefeller.edu>:
Hi Doug, so I made contrast matrices and stored them in mystudy, and then ran selxavg3-sess per subject. I defined three different contrasts (in three mat files), but selxacg3-sess only gives me one analysis, it seems to be an F-test. When I do isxconcat-sess after that, I get six ces files per analysis (I presume one for each of my predictors), not three (number of contrasts). Is there a way for me to force selxavg3-sess to actually compute the contrasts that I want? Thanks, Caspar 2014-11-13 12:16 GMT-05:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: I don't know whether that will work or not. If it runs, you can compare the result to computing the contrast manually to see if there is a difference. If there is no difference, then it works. On 11/13/2014 10:18 AM, Caspar M. Schwiedrzik wrote: > Hi Doug, > coming back to this once more. I am thinking that I can bypass > mkcontrast-sess entirely if I provide a contrast matrix that has > ContrastMtx_0 and WCond set to the contrast that I am interested in. > For example [1 -0.2 -0.2 -0.2 -0.2 -0.2] to contrast my first > continuous predictor and against the remaining five continuous > predictors. > For that, I would just place a corresponding mat file in a > subdirectory in mystudy. > Is there anything that speaks that and anything else that I need to > consider? > Thanks! > Caspar > > > > > > 2014-11-11 16:37 GMT-05:00 Caspar M. Schwiedrzik > <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>: > > Hi Doug, > I am a little bit confused about the variance. Shouldn't the > relevant variance be the variance over the differences, not the > mean variance over all? > Of course at the level of ces and cesvar, I do not have access to > the timepoint by timepoint differences anymore. > Is there another way to do this? > Thanks, Caspar > > > 2014-11-11 13:54 GMT-05:00 Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>: > > yes > On 11/11/2014 01:28 PM, Caspar M. Schwiedrzik wrote: > > Hi Doug, > > just to clarify: > > If I want to contrast taskreg 1 vs. mean(taskreg 2,3,4,5,6), > I would > > compute > > ces= ces(taskreg 1) - mean(ces(taskreg 2,3,4,5,6)) > > and > > cesvar=mean(cesvar(taskreg(1,2,3,4,5,6))) > > > > Is that correct? > > Thanks, Caspar > > > > > > 2014-11-11 13:19 GMT-05:00 Bill Taylor <bt@cs.wisc.edu <mailto:bt@cs.wisc.edu> > <mailto:bt@cs.wisc.edu <mailto:bt@cs.wisc.edu>> > > <mailto:bt@cs.wisc.edu <mailto:bt@cs.wisc.edu> <mailto:bt@cs.wisc.edu <mailto:bt@cs.wisc.edu>>>>: > > > > Sorry, Though we do have freesurfer pipelines we run in > Madison, I > > responded to wrong email. > > > > Bill Taylor > > Center for High Throughput Computing > > Computer Sciences > > University of Wisconsin, Madison > > > > On 11/11/2014 12:09 PM, Bill Taylor wrote: > > > I'll start the process thursday. > > > On 11/11/2014 12:04 PM, Douglas N Greve wrote: > > >> It will be the same as the DOF of the individual > contrasts > > (don't sum them). > > >> > > >> On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote: > > >>> ok, I will try that. How do I get the degrees of > freedom? > > Thanks! Caspar > > >>> > > >>> 2014-11-11 12:04 GMT-05:00 Douglas N Greve > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>>: > > >>> > > >>> > > >>> Actually, you can still do each contrast > individually. > > Each will > > >>> produce > > >>> ces and cesvar files. Take the difference > between the > > ces files > > >>> and the > > >>> average of the cesvar files, then feed the > result into > > mri_glmfit FFX > > >>> > > >>> doug > > >>> > > >>> > > >>> On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik > wrote: > > >>> > Hi Doug, > > >>> > I wanted to follow up on this. Would you be > able to > > provide a > > >>> > workaround for contrasting multiple taskregs > against > > each other? Is > > >>> > there something I can try in the meantime? > Thanks, Caspar > > >>> > > > >>> > > > >>> > 2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik > > >>> > <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>> > > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>> > > >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>> > > >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>>>>: > > >>> > > > >>> > Hi Doug, > > >>> > thanks for your reply. I would like to > feed the > > differences > > >>> into a > > >>> > FFX group analysis, so I think I will > need to > > resort to your > > >>> > workaround. It would be great if you could > provide > > that. Thanks! > > >>> > Caspar > > >>> > > > >>> > 2014-11-10 13:45 GMT-05:00 Douglas N Greve > > >>> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>>>: > > >>> > > > >>> > > > >>> > To get sig maps for an individual, > this is > > problematic > > >>> but I > > >>> > could > > >>> > probably come up with a work-around. For a > group > > >>> analysis, you can > > >>> > simply compute each taskreg separately, then > > subtract > > >>> the two > > >>> > prior to > > >>> > running mri_glmfit. > > >>> > doug > > >>> > > > >>> > On 11/10/2014 01:36 PM, Caspar M. > Schwiedrzik > > wrote: > > >>> > > Hi! > > >>> > > A quick follow-up: > > >>> > > I have a taskreg file with 6 > continuous > > predictors. I > > >>> would > > >>> > like to > > >>> > > run specific contrasts, e.g., > predictor 1 vs. > > >>> mean(predictor > > >>> > 2:6). > > >>> > > From what I gather, selxavg3-sess > will run > > automatic > > >>> > contrasts on > > >>> > > taskregs, but the automatic > contrasts are > > against > > >>> baseline. > > >>> > This is > > >>> > > not what I need at this point. > > >>> > > mk-contrast-sess does not like > what I am > > putting in > > >>> because > > >>> > I do not > > >>> > > have a paradigm file in which > condition > > numbers are > > >>> specified. > > >>> > > Is there a way to compute specific > contrasts > > between > > >>> multiple > > >>> > > taskregs, and if not, is there a > workaround? > > >>> > > Thank you very much, Caspar > > >>> > > > > >>> > > > > >>> > > 2014-11-06 15:23 GMT-05:00 Caspar > M. Schwiedrzik > > >>> > > <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>> > > >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>> > > >>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>> > > >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>>> > > >>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>> > > >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>> > > >>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>> > > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>>>>>: > > >>> > > > > >>> > > Hi! > > >>> > > I have several external > regressors in my > > analysis > > >>> that I > > >>> > configure > > >>> > > with -taskreg in mkanalysis-sess > > (something like > > >>> -notask > > >>> > -taskreg > > >>> > > nameoffile 6). > > >>> > > I was wondering how to set up > > mkcontrast-sess to > > >>> > contrast these > > >>> > > regerssors given that I do not > have a > > paradigm > > >>> file for > > >>> > them. > > >>> > > Can I just do something like -a > 1 -c 2 > > -c 3 -c 4 -c 5? > > >>> > > > > >>> > > Thanks, Caspar > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > _______________________________________________ > > >>> > > Freesurfer mailing list > > >>> > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > >>> > > > > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>> > > > >>> > -- > > >>> > Douglas N. Greve, Ph.D. > > >>> > MGH-NMR Center > > >>> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>> > > >>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>>> > > >>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>>>> > > >>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>> > > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>>> <tel:617-726-7422 <tel:617-726-7422> > > <tel:617-726-7422 <tel:617-726-7422>> > > >>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>>> > > >>> > > > >>> > Bugs: > > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > >>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > >>> > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > >>> > FileDrop: > > https://gate.nmr.mgh.harvard.edu/filedrop2 > > >>> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > >>> > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > >>> > > > >>> > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > >>> > Outgoing: > > >>> > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > >>> > > > >>> > _______________________________________________ > > >>> > Freesurfer mailing list > > >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > >>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>> > > > >>> > > > >>> > The information in this e-mail is > intended > > only for the > > >>> person > > >>> > to whom it is > > >>> > addressed. If you believe this e-mail was sent > > to you in > > >>> error > > >>> > and the e-mail > > >>> > contains patient information, please contact > > the Partners > > >>> > Compliance HelpLine at > > >>> > http://www.partners.org/complianceline . If > the e-mail was > > >>> > sent to you in error > > >>> > but does not contain patient > information, > > please contact the > > >>> > sender and properly > > >>> > dispose of the e-mail. > > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> > _______________________________________________ > > >>> > Freesurfer mailing list > > >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>> > > >>> -- > > >>> Douglas N. Greve, Ph.D. > > >>> MGH-NMR Center > > >>> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > >>> Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > > >>> Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 > <tel:617-726-7422> > > <tel:617-726-7422 <tel:617-726-7422>>> > > >>> > > >>> Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > >>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > >>> FileDrop: > https://gate.nmr.mgh.harvard.edu/filedrop2 > > >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > >>> > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > >>> Outgoing: > > >>> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > >>> > > >>> _______________________________________________ > > >>> Freesurfer mailing list > > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>> > > >>> > > >>> > > >>> > > >>> _______________________________________________ > > >>> Freesurfer mailing list > > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
4216
Age (days ago)
4227
Last active (days ago)
freesurfer@nmr.mgh.harvard.edu
17 comments
3 participants
participants (3)
-
Bill Taylor -
Caspar M. Schwiedrzik -
Douglas N Greve